Microbial Cell Factories最新文献

{"title":"Harnessing the endophytic Clavispora lusitaniae for the biogenic synthesis of ethylene glycol-capped cerium oxide nanoparticles: a green approach to combat respiratory Pseudomonas aeruginosa.","authors":"Hoda S Nouh, Nessma A El-Zawawy, Shimaa El-Sapagh, Ebrahim M Shalamesh, Sally M Metwally","doi":"10.1186/s12934-026-03091-x","DOIUrl":"https://doi.org/10.1186/s12934-026-03091-x","url":null,"abstract":"<p><strong>Background: </strong>The utilization of endophytes as specialized microbial cell factories offers a sustainable and high-efficiency platform for the biosynthesis of functionalized nanomaterials. This study investigates the potential of a novel endophytic yeast, Clavispora lusitaniae, to produce cerium oxide nanoparticles (CeO₂NPs) and evaluates their efficacy against extensively drug-resistant (XDR) P. aeruginosa.</p><p><strong>Results: </strong>An endophytic yeast, C. lusitaniae, was isolated for the first time from the medicinal plant Artemisia judaica and employed for the biosynthesis of CeO₂NPs, followed by surface capping with ethylene glycol (EG) to modify the nanoparticle surface properties. The synthesized nanoparticles were characterized using UV-Vis, FTIR, XRD, TEM, and DLS. These analyses confirmed the formation of spherical EG-CeO₂NPs with an average size of 8-20 nm. EG-CeO₂NPs exhibited strong antibacterial activity against XDR P. aeruginosa strains, with a minimum inhibitory concentration ranging from 0.6 to 1.25 mg/mL. Furthermore, these nanoparticles demonstrated potent anti-biofilm efficacy, achieving reductions of up to 89%. Mechanistic investigations demonstrated that EG-CeO₂NPs disrupt bacterial cell membranes, leading to intracellular protein leakage and elevated lipid peroxidation (indicated by increased malondialdehyde levels). Furthermore, the expression levels of quorum sensing (e.g., lasR and rhlR) and virulence-associated genes (e.g., toxA and exoS) were markedly downregulated by up to 87% compared to untreated controls.</p><p><strong>Conclusions: </strong>This study establishes C. lusitaniae as a robust microbial cell factory for synthesizing functionalized CeO₂NPs with potent activity against XDR P. aeruginosa. Our results demonstrate the potential of microbial bioprocessing in engineering prospective nanotechnological platforms to combat antimicrobial resistance. However, further studies evaluating colloidal behavior under physiologically relevant conditions, mammalian-cell cytotoxicity, and in vivo efficacy are required before biomedical translation.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13495233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of RIM15 deletion on yeast adaptation to synthetic spruce hydrolysate.","authors":"Nathália Vilela, Cecilia Trivellin, Luca T Pianale, Julie Brouchon, Julien Patrouix, Diana Ekman, Simon Trancart, Lisbeth Olsson","doi":"10.1186/s12934-026-03096-6","DOIUrl":"10.1186/s12934-026-03096-6","url":null,"abstract":"<p><p>Microbial robustness (i.e., to keep the same performance in the face of several perturbations) is a desirable trait for industrial yeasts, particularly in second-generation bioethanol production, where inhibitory compounds in lignocellulosic hydrolysates impair microbial performance. In this study, we investigated the role of the stress-responsive kinase Rim15 in stress adaptation and robustness by subjecting Saccharomyces cerevisiae wild-type (WT) and rim15Δ strain to adaptive laboratory evolution (ALE) in synthetic spruce hydrolysate (SSH). This hydrolysate contains high concentrations of inhibitory compounds, such as acetic acid and 5-hydroxymethylfurfural. Crucially, ALE consisted of two steps, including a medium swap regime that enabled adaptation to 100% SSH. Although WT and rim15Δ strain followed distinct evolutionary trajectories during ALE, both strains improved growth performance and robustness on SSH. The ability of the rim15Δ strain to adapt to 100% SSH was associated with impaired daughter cell separation and multicellular clump formation. Genome sequencing identified a mutation in a morphogenetic gene (ACE2) in Evolved rim15Δ. This differed from mutations in key transcriptional regulators (e.g., SSN8, SSN2) identified in Evolved WT. Reverse engineering indicated that ACE2 loss-of-function contributes to the multicellular clumping phenotype of the Evolved rim15Δ strain, while deletion mutants of SSN2 and SSN8 exhibited improved growth in SSH compared to the parental strain. Together, these findings indicate that yeast robustness can emerge through distinct adaptive strategies shaped by the genetic background, involving transcriptional rewiring or morphogenetic adaptation to lignocellulosic stress.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148765152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bio-process development for sustainable, large-scale production of LAB-oligosaccharides as a potential anti-colon-cancer metabolites produced by Lactobacillus acidophilus 20079.","authors":"Ahmed M Kenawy, Gaber A Abo-Zaid, Tarek H Taha, Amany E Ragab, Lamiaa A Al-Madboly, Nehal M El-Deeb","doi":"10.1186/s12934-026-03067-x","DOIUrl":"https://doi.org/10.1186/s12934-026-03067-x","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Lactic acid bacteria and their metabolites have shown promising biological activities against different types of cancer, esspecially, colon cancer. In our previouse study, we extracted and optimized the production of a mixture of three oligosaccharides from Lactobacillus acidophilus DSMZ 20079 at the laboratory scale using statistical experimental designs and the active oligosaccharide HPLC fraction was identified as LA-EPS-20079. Also, the anticancer activity of the extracted LA-EPS-20079 against colon cancer CaCo-2 cell line was confirmed via the downregulation of the gene expression of Bcl2 and Survivin genes (6). In the present study, we produced a mixture of bioactive oligosaccharides from L. acidophilus DSMZ 20079 in 10 L bioreactor that maintained the anti-colon cancer against CaCo-2 cell line effects, which is a major transition towards the semi industrial level. To that end, a batch fermentation was carried out in a 10 L bioreactor under uncontrolled pH condition, starting at pH 6.0. During the fermentation process, the bacterial cell mass was increased exponentially with a constant specific growth rate (µ) of 0.07 h&lt;sup&gt;-1&lt;/sup&gt;, reaching a maximum biomass of 6.93 g L&lt;sup&gt;-1&lt;/sup&gt; at 44 h. Also, the concentration of the produced total exooligosaccharides gradually increased and reached a maximum concentration of 1461.43 µg mL&lt;sup&gt;-1&lt;/sup&gt; at 40 h post-incubation. Furthermore, the glucose consumption rate was 1.21 g L&lt;sup&gt;-1&lt;/sup&gt; h&lt;sup&gt;-1&lt;/sup&gt;, while the LAB-oligosaccharide production rate reached 96.22 µg mL&lt;sup&gt;-1&lt;/sup&gt; h&lt;sup&gt;-1&lt;/sup&gt;. Moreover, oligosaccharides chemical composition was studied after scaling up the production process using 1D and 2D proton and carbon NMR, along with monomeric composition analysis. The results indicated that LAB-oligosaccharide is a mixture of oligosaccharides, not a single structure, and the mixture consists of three monomeric sugars; herein, we referred to the oligosaccharide mixture as LAB-oligosaccharide. Additionally, the anticancer activity of LAB- oligosaccharide was tested in samples collected from the bioreactor at 0, 12, 14, 16, 18, 20, 22, 24, 36, 40 and 44 h time points against the CaCo-2 cancer cell line. The results confirmed the in-vitro anticancer activity with maximum inhibition percentages of 72.01% and 81.7% after 22 and 24 h, respectively. On the other hand, to establish an environmentally friendly production process, we evaluated the efficacy of using the bacterial biomass residue after LAB- oligosaccharide extraction as a substrate for bacterial isolates growth to produce industrially important enzymes (Lipases and proteases). In this context, 5 bacterial isolates were found to produce both enzymes. These bacterial isolates were characterized using 16S-rRNA gene sequencing and the relatedness between the isolates was studied using phylogenetic analysis. The results demonstrated that the residual biomass supported the growth of B. subtillis PX205316 (2F) for the production o","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13474794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148759775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Filamentous multiscale characterization of the cultivation of Actinomadura namibiensis pellets for model-based prediction of labyrinthopeptin A1 biosynthesis.","authors":"Qiyue Liu, Zuzanna Justyna Kozanecka, Jintian Liu, Katrin Dohnt, Rainer Krull, Markus Böl","doi":"10.1186/s12934-026-03088-6","DOIUrl":"10.1186/s12934-026-03088-6","url":null,"abstract":"<p><p>The filamentous actinomycete Actinomadura namibiensis has attracted increasing interest as the only known natural producer of the carbocyclic lantibiotic labyrinthopeptin A1, a secondary metabolite with a broad antiviral spectrum of activity. Developing a model of microbial growth and product formation at the pellet level requires a deeper mechanistic understanding of the interactions between cultivation conditions, substrate availability, and oxygen limitation. These factors influence the cultivation process and product formation. As part of this work, a predictive model in the form of diffusion-reaction equations is developed to quantitatively describe nutrient uptake, oxygen diffusion limitation, and pellet growth. This framework couples the consumption kinetics of carbon sources, such as glucose and glycerol, to pellet growth, maintenance metabolism, and the formation of the secondary metabolite labyrinthopeptin A1. The model is calibrated based on the results of multiscale experiments, i.e., offline analysis of shake flask cultures and oxygen profiling of pellets at different time points under various conditions. This forms the basis for understanding nutrient uptake, metabolic heterogeneity, and mass transfer limitations within the pellets. Thus, the model provides a quantitative basis for predicting productivity. The validated multiscale model reproduces the experimental results well and can be used to predict pellet growth, substrate uptake, and product formation.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-cell surface-display system in attenuated Salmonella Enteritidis for slide microagglutination-based antibody detection.","authors":"Yacory Sernaque-Aguilar, Dora Rios-Matos, Astrid Poma-Acevedo, Alen Zimic-Sheen, María Belén-Balta, Ricardo Choque-Guevara, Ricardo Montesinos-Millán, Mario I Salguedo-Bohorquez, Gisela Isasi-Rivas, Angela Montalván-Avalos, Freddy Ygnacio-Aguirre, Julio Ticona, Manolo Fernández-Sánchez, Manolo Fernández-Díaz, Mirko Zimic","doi":"10.1186/s12934-026-03083-x","DOIUrl":"https://doi.org/10.1186/s12934-026-03083-x","url":null,"abstract":"<p><strong>Background: </strong>Microagglutination is a sensitive, rapid, and cost-effective serological assay widely used for disease diagnosis and surveillance in animals and humans. However, it traditionally relies on culturing live pathogenic bacteria as antigens, posing biosafety risks and limiting its application primarily to bacterial pathogens. Bacterial surface display technology offers a promising alternative by enabling the presentation of heterologous proteins or peptides on the bacterial surface, avoiding the need to culture the target pathogen, simplifying antigen preparation, and enabling potential diagnostic applications for non-bacterial pathogens. Despite these advantages, integration of this technology with slide-based microagglutination assays has not yet been evaluated. In this proof-of-concept, we evaluated a surface display platform in attenuated Salmonella Enteritidis for antibody detection by slide microagglutination, using the nucleocapsid (N) protein of Infectious Bronchitis Virus (IBV) as a model antigen.</p><p><strong>Results: </strong>The IBV N protein was fused to the N-terminal anchor domain of the ice nucleation protein (INP) and cloned into pET-28a. The resulting INP_N fusion protein was expressed in attenuated Salmonella Enteritidis, and its surface exposure was evaluated by immunofluorescence and flow cytometry on non-permeabilized cells, with flow cytometry indicating a surface display efficiency of 96.5%. Slide microagglutination was performed using 50 hen sera and inactivated Salmonella Enteritidis cells presenting surface-exposed N protein. This assay identified all positive sera and 20 of 25 negative sera, showing substantial agreement with the reference ELISA (κ = 0.8), with preliminary estimates of 100% sensitivity (95% CI, 87-100%) and 80% specificity (95% CI, 61-91%). No cross-reactivity was observed with commercial antisera against pathogens unrelated to IBV.</p><p><strong>Conclusions: </strong>The attenuated Salmonella surface-display platform integrated into a slide microagglutination assay showed preliminary feasibility for antibody detection under the conditions evaluated. This approach does not require live pathogen cultivation, specialized equipment, antigen purification, or chemical conjugation steps. However, further optimization is needed to improve the platform's display efficiency and enhance specificity without compromising sensitivity. In addition, evaluation using a larger and more diverse sample set, including field samples, is required to further assess the performance and potential applicability of the assay.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eliminating manganese sensitivity and boosting citric acid production in Aspergillus niger through transporters manipulation.","authors":"Alexandra Márton, Josee Vandal, Vivien Bíró, Erzsébet Fekete, Erzsébet Sándor, Béla Kovács, Adrian Tsang, Levente Karaffa","doi":"10.1186/s12934-026-03082-y","DOIUrl":"10.1186/s12934-026-03082-y","url":null,"abstract":"<p><strong>Background: </strong>Citric acid, a high-volume bioproduct, is manufactured by submerged fermentation using the filamentous fungus Aspergillus niger. Citric acid overflow requires Mn(II) ion concentrations not exceeding 5 µg L^- 1. However, manganese easily leaches from media ingredients or stainless-steel bioreactors, necessitating costly, laborious removal.</p><p><strong>Results: </strong>Aspergillus niger citrate fermentations were evaluated across varied manganese profiles, comparing a novel double transporter mutant against parental and single-mutant strains. This strain overexpresses cexA - the primary plasma membrane exporter whose activity overcomes a major production bottleneck - under the control of the strong glaA promoter in a background deficient in dmtA, which encodes the primary high-affinity NRAMP-family manganese transporter. Under high-manganese conditions (100-165 µg L^- 1) simulating industrial substrate impurities and bioreactor leaching, the double transporter mutant outperformed the other strains. Despite abundant manganese that triggers high biomass (50 g L^- 1) and low citrate yields in the parental strain NRRL2270, this cell factory maintained high-yield overflow metabolism. Driven by an accelerated maximal glucose consumption rate of 1.61 g L^- 1 h^- 1 and reduced biomass accumulation (9.1 g L^- 1), it accumulated citric acid to levels comparable to those achieved under manganese deficiency. The double transporter mutant compressed the fermentation period by 17% (from 300 to 250 h), minimizing operational energy and utility costs and significantly enhancing overall productivity. To validate industrial scalability, the untreated, high-manganese process was replicated in 15-L stainless steel bioreactors - accounting for up to 30 µg L^- 1 of manganese leaching - and successfully scaled up by an order of magnitude in a 150-L bioreactor. Carbon balance closures within ± 5% confirmed no appreciable by-product formation.</p><p><strong>Conclusions: </strong>By demonstrating the maintenance of high-yield overflow metabolism under manganese-replete conditions, alongside enhanced productivity through shortened fermentation times across different vessel scales, this study establishes this A. niger mutant as an attractive cell factory for industrial applications.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive laboratory evolution of Saccharomyces cerevisiae enhances butyric acid tolerance and enables co-cultivation with Clostridium tyrobutyricum.","authors":"K Oehlenschläger, S Bauschatz, E Schepp, D Holtmann, R Ulber","doi":"10.1186/s12934-026-03078-8","DOIUrl":"10.1186/s12934-026-03078-8","url":null,"abstract":"<p><p>Adaptive laboratory evolution (ALE) was successfully applied to improve the tolerance of Saccharomyces cerevisiae toward butyric acid, enabling its use in co-culture with Clostridium tyrobutyricum for the simultaneous production of ethanol and butyric acid as ester precursors. S. cerevisiae was adapted through serial transfer at progressively increasing butyric acid concentrations up to 20 g L⁻¹. The evolved yeast population exhibited significantly enhanced butyric acid tolerance and maintained ethanol production under acid-stress conditions. Interestingly, the evolved population also displayed increased maximum glucose consumption rate and ethanol productivity under non-stress conditions. Whole-genome variant analysis was performed by comparing the wild-type strain, an intermediate evolved population and the final evolved population obtained during ALE. The results suggest that adaptation may be associated with changes in regulatory processes, cellular homeostasis, and membrane and cell wall remodeling. The co-culture with the acid producer C. tyrobutyricum demonstrated efficient and balanced substrate utilization, indicating a stable division of labor between the two organisms. Fed-batch cultivation yielded 20.31 ± 2.43 g L⁻¹ butyric acid and 28.18 ± 3.37 g L⁻¹ ethanol. With the evolved yeast, ethanol concentrations increased fourfold compared to those achieved with the wild-type strain in previous studies, underscoring the potential of ALE to overcome limitations in co-culture systems.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13436328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148670049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.","authors":"Anna Detman-Ignatowska, Gabriele Schiro, Rafał Filip, Emilia Samborowska, Jakub Karczmarski, Sara Jarmakiewicz-Czaja, Kinga Jakubowska, Anna Williams, Nabahi Ramos Hickman, Daniel Laubitz, Anna Sikora","doi":"10.1186/s12934-026-03052-4","DOIUrl":"10.1186/s12934-026-03052-4","url":null,"abstract":"<p><strong>Background: </strong>Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.</p><p><strong>Results: </strong>HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.</p><p><strong>Conclusions: </strong>Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13625237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fine-tuned synthetic transcription factors for production of 3'-phosphoadenosine-5'-phosphosulfate in yeast.","authors":"Madhushruti Borah, Shanna Gu, Essa M Saied, Christoph Arenz, Mattheos Koffas, Gita Naseri","doi":"10.1186/s12934-026-03072-0","DOIUrl":"10.1186/s12934-026-03072-0","url":null,"abstract":"<p><strong>Background: </strong>Technologies developed over the past decade have made Saccharomyces cerevisiae a promising platform for producing various natural products. Balancing multi-enzyme expression, while maintaining robust microbial growth, remains a limiting factor for engineering long biosynthetic pathways in yeast.</p><p><strong>Result: </strong>Here, we improved the transcriptional capacity of our previously developed synthetic transcription factors (synTFs) derived from the plant JUB1 DNA-binding domain, whose expression is controlled by an β-D-1-thiogalactopyranoside (IPTG)-inducible promoter. To this end, at cysteine positions within surface-exposed loop regions of a JUB1-derived DNA-binding scaffold, we introduced a short peptide to enhance loop flexibility while providing local stability and orientation. The generated synTFs, so-called JUB1-X synTFs, varying in strength, have been successfully used to improve the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS), a universal sulfate donor necessary for the synthesis of therapeutic glycosaminoglycans and sulfolipids, in yeast. Using the generated yeast strain, in simple batch culture, PAPS accumulation of 21.4 ± 5.8 mg g⁻¹ cdw was achieved after only 5 h of inducing the expression of JUB1-X synTFs.</p><p><strong>Conclusions: </strong>The design principle demonstrated here provides a generalizable strategy to fine-tune other synTFs derived from heterologous DNA-binding domains, expanding the regulatory capabilities of existing synTF collections. Together, this work offers a modular, scalable approach to constructing high-performance gene circuits and supports the development of yeast cell factories for the synthesis of complex natural products.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification, functional characterization of a novel flavohemoglobin from Ensifer adhaerens and its application to enhancing vitamin B₁₂ production.","authors":"Jinmei Zhu, Shiyu Wang, Bo Li, Bolun Wang, Ping Wang, Jiequn Wu, Zejian Wang","doi":"10.1186/s12934-026-03073-z","DOIUrl":"10.1186/s12934-026-03073-z","url":null,"abstract":"<p><strong>Background: </strong>Bacterial flavohemoglobins are well-characterized as versatile proteins that significantly augment the biosynthesis yields of diverse value-added compounds in engineered microbial platforms. Our previous studies revealed marked upregulation of a flavohemoglobin-encoding gene in Ensifer adhaerens under oxygen-limiting conditions, with potential associations to vitamin B₁₂ production.</p><p><strong>Results: </strong>In this study, a novel flavohemoglobin (FHP, encoded by b12fla gene) from Ensifer adhaerens were characterized. FHP exhibited high sequence and structural similarity to HMP (the flavohaemoglobin from Halalkalibacterium halodurans), yet demonstrating 3-fold higher NADH oxidase activity. Heterologous expression of FHP in Escherichia coli positively influences cell growth, biomass yield on carbon and nitrogen sources, increased OD₆₀₀ and Oxygen Uptake Rate (OUR) in 50-L fermenter of FHP-expressing strain EcFHP (12% and 65% higher compared with control strain respectively). In addition, SEM analysis revealed that cells of overexpression strains exhibited obvious morphological alterations, manifesting as longitudinal extension or radial expansion compared to cells of wild-type strain. Overexpression of b12fla gene in E. adhaerens Casida A generated the recombinant strain Ea-b12fla, which produced 323 mg L^- 1 of vitamin B₁₂ in a 50-L fermentation while the wild-type strain yielded only 247 mg L^- 1. Furthermore, cell growth, OUR, Carbon-dioxide Escape Rate (CER) and sugar utilization were obviously enhanced by overexpression of the flavohemoglobin.</p><p><strong>Conclusions: </strong>A flavohemoglobin from a new source was identified in this study. Heterologous expression in E. coli validated its ability to promote cell growth under specific oxygen supply conditions. Overexpression in E. adhaerens significantly enhanced cell growth and cell metabolism, while markedly increasing vitamin B₁₂ production. Collectively, these findings demonstrate that flavohemoglobin (FHP) enhances cellular oxygen utilization while simultaneously improving the assimilation efficiency of carbon and nitrogen sources, and reveal the potential of flavohemoglobin for applications in high-density fermentation processes.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13685156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}